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Update geo-fixes #279

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Sep 27, 2024
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Update geo-fixes #279

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6 changes: 6 additions & 0 deletions ingest/defaults/geolocation-rules.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -14,3 +14,9 @@ Europe/Italy/Fvg/Gorizia Europe/Italy/Friuli Venezia Giulia/Gorizia
# Unclear which location is the real location
Europe/Netherlands/Utrecht/Rotterdam Europe/Netherlands//
North America/USA/Washington/Dc North America/USA/Washington DC/
# Following renamings as part of work on INRB Clade-I builds
Africa/Democratic Republic of the Congo/*/Nyagezi Africa/Democratic Republic of the Congo/*/Nyangezi
# Note that in our master geolocation rules we replace "Sud-Kivu" with "Sud Kivu" (similarly for "Nord-Kivu")
# however the INRB tends to use "Sud-Kivu". We can't add a rule here to change it back (`augur curate` doesn't
# allow it) so we enforce the use of "Sud Kivu" in INRB data as well.
Comment on lines +19 to +21
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I was curious what you meant by "augur curate doesn't allow it"...Because we just concatenate these to the "general" geolocation rules, the conflicting rules raises the CyclicGeolocationRulesError in augur curate apply-geolocation-rules.

Not sure if this is something we should handle within Augur or if the workflow should be improved to not blindly concatenate the geolocation rules...

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Not sure if this is something we should handle within Augur...

If we're going to continue with the pattern of a master-list plus some repo-specific additions it'd be nice if those additions could function as overrides. I.e. if the master list replaces X with Y, we could add an override of Y to X (or Y to Z etc) in a repo-specific manner.

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Yeah, that makes sense! Tracking in nextstrain/augur#1648.

Africa/Democratic Republic of the Congo/South Kivu/* Africa/Democratic Republic of the Congo/Sud Kivu/*